represents a single pool used by quota selector More...

#include <SecondaryStructurePool.hh>

Public Member Functions
	SecondaryStructurePool (Size, std::string, char, utility::vector1< Size > &, utility::vector1< Real > &, Real, Size, Size)
	Creates a pool of a given size and name. More...

char	get_ss_type () const

virtual	~SecondaryStructurePool ()

virtual Size	total_size () const
	Says how many fragments (in total) may fit into this pool. More...

virtual Size	current_size () const
	Says how many fragments are currently in this pool. More...

virtual Size	size_left () const
	Says how many fragments can still be inserted into this pool. More...

virtual bool	could_be_accepted (ScoredCandidate) const

virtual void	push (ScoredCandidate candidate)
	Push a fragment candidate into the container. More...

virtual bool	add (ScoredCandidate)
	Insert a fragment candidate to the container. More...

void	clear ()
	removes all candidates from the container More...

Size	count_candidates (Size) const
	Check how many candidates have been already collected for a given position. More...

Size	count_candidates () const
	Check how many candidates have been already collected for all positions. More...

Size	query_length () const
	Check the size of query sequence that this object knows. More...

void	insert (Size, CandidatesCollectorOP collector)
	Inserts candidates from another Collector for a give position in the query Candidates may or may not get inserted depending on the candidate. More...

ScoredCandidatesVector1 &	get_candidates (Size)
	Returns all the candidate in this pool. More...

void	resize (Size new_size)

void	print_report (std::ostream &, scores::FragmentScoreManagerOP) const
	Describes what has been collected. More...

virtual void	set_fraction (Real new_fraction)
	Sets the fraction of this quota pool in the entire population of fragments. More...

virtual Real	quota_score (ScoredCandidate candidate) const
	provides the score for a candidate that was used to sort a quota pool More...

Public Member Functions inherited from protocols::frag_picker::quota::QuotaPool
	QuotaPool (std::string pool_name, Real quota_fraction)
	Creates a pool of a given size and name. More...

virtual	~QuotaPool ()

std::string const &	get_pool_name () const
	returns the name assigned to this quota pool More...

virtual void	show_availability (std::ostream &where) const
	prints information on which fragments can be accepted by this pool and how many of them More...

Real	get_fraction () const
	returns the fraction of this quota pool in the entire population of fragments More...

Private Attributes
Size	total_size_

Size	this_size_

char	ss_type_

utility::vector1< Size >	components_

utility::vector1< Real >	weights_

BoundedQuotaContainerOP	storage_

Size	buffer_factor_

Detailed Description

represents a single pool used by quota selector

Constructor & Destructor Documentation

protocols::frag_picker::quota::SecondaryStructurePool::SecondaryStructurePool	(	Size	total_size,
		std::string	pool_name,
		char	ss_type,
		utility::vector1< Size > &	which_components,
		utility::vector1< Real > &	weights,
		Real	fraction,
		Size	n_scores,
		Size	buffer_factor = `5`
	)

Creates a pool of a given size and name.

Parameters

size	- total number of fragments from all the pools at a given position
name	- name assigned to this pool. This in general may be any string that later allows one control pool's behavior from a flag file
ss_type	- what is the type of secondary structur this pool is accepting
score_components_id	- which scores will be used to sort this pool
weights	- weights for the scores that in general may be different than these used for fragment picking
fraction	- fraction of this pool in the entire population
total_size	- how many fragments will be selected (in total in all pools)
name	- name assigned to this pool. This in general may be any string that later allows one control pool's behavior from a flag file
ss_type	- what is the type of secondary structur this pool is accepting
fraction	- fraction of the total number of fragments that goes into this pool

References buffer_factor_, components_, ss_type_, storage_, this_size_, total_size(), total_size_, protocols::frag_picker::quota::trSecondaryStructurePool, and weights_.

protocols::frag_picker::quota::SecondaryStructurePool::~SecondaryStructurePool ( )

virtual

Member Function Documentation

bool protocols::frag_picker::quota::SecondaryStructurePool::add ( ScoredCandidate candidate )

virtual

Insert a fragment candidate to the container.

Implements protocols::frag_picker::CandidatesCollector.

References ss_type_, and storage_.

void protocols::frag_picker::quota::SecondaryStructurePool::clear ( )

inlinevirtual

removes all candidates from the container

Implements protocols::frag_picker::quota::QuotaPool.

References storage_.

bool protocols::frag_picker::quota::SecondaryStructurePool::could_be_accepted ( ScoredCandidate candidate ) const

virtual

Implements protocols::frag_picker::quota::QuotaPool.

References ss_type_.

Size protocols::frag_picker::quota::SecondaryStructurePool::count_candidates ( Size ) const

inlinevirtual

Check how many candidates have been already collected for a given position.

Detailed: This is a very special case - collector will be used only for a given position.: Thus it returns the total number of inserted candidates, as count_candidates() does

Implements protocols::frag_picker::CandidatesCollector.

References current_size().

Size protocols::frag_picker::quota::SecondaryStructurePool::count_candidates ( ) const

inlinevirtual

Check how many candidates have been already collected for all positions.

Implements protocols::frag_picker::quota::QuotaPool.

References current_size().

virtual Size protocols::frag_picker::quota::SecondaryStructurePool::current_size ( ) const

inlinevirtual

Says how many fragments are currently in this pool.

Implements protocols::frag_picker::quota::QuotaPool.

References storage_.

Referenced by count_candidates(), print_report(), and size_left().

ScoredCandidatesVector1& protocols::frag_picker::quota::SecondaryStructurePool::get_candidates ( Size )

inlinevirtual

Returns all the candidate in this pool.

Implements protocols::frag_picker::CandidatesCollector.

References storage_.

char protocols::frag_picker::quota::SecondaryStructurePool::get_ss_type ( ) const

inline

References ss_type_.

void protocols::frag_picker::quota::SecondaryStructurePool::insert	(	Size	,
		CandidatesCollectorOP	collector
	)

inlinevirtual

Inserts candidates from another Collector for a give position in the query Candidates may or may not get inserted depending on the candidate.

Implements protocols::frag_picker::CandidatesCollector.

References c, l, storage_, and utility_exit_with_message.

void protocols::frag_picker::quota::SecondaryStructurePool::print_report	(	std::ostream &	out,
		scores::FragmentScoreManagerOP
	)		const

virtual

Describes what has been collected.

Implements protocols::frag_picker::CandidatesCollector.

References current_size(), protocols::frag_picker::quota::QuotaPool::get_pool_name(), and ss_type_.

virtual void protocols::frag_picker::quota::SecondaryStructurePool::push ( ScoredCandidate candidate )

inlinevirtual

Push a fragment candidate into the container.

Implements protocols::frag_picker::quota::QuotaPool.

References storage_.

Size protocols::frag_picker::quota::SecondaryStructurePool::query_length ( ) const

inlinevirtual

Check the size of query sequence that this object knows.

Detailed: This is a very special case - collector will be used only for a given position and it does NOT: know the tolal size. Thus it returns always 0

Implements protocols::frag_picker::CandidatesCollector.

virtual Real protocols::frag_picker::quota::SecondaryStructurePool::quota_score ( ScoredCandidate candidate ) const

inlinevirtual

provides the score for a candidate that was used to sort a quota pool

Detailed: This base class returns the most recent total score for a fragment

Reimplemented from protocols::frag_picker::quota::QuotaPool.

References components_, and weights_.

void protocols::frag_picker::quota::SecondaryStructurePool::resize ( Size new_size )

inline

References buffer_factor_, and storage_.

virtual void protocols::frag_picker::quota::SecondaryStructurePool::set_fraction ( Real new_fraction )

inlinevirtual

Sets the fraction of this quota pool in the entire population of fragments.

Reimplemented from protocols::frag_picker::quota::QuotaPool.

References buffer_factor_, protocols::frag_picker::quota::QuotaPool::set_fraction(), storage_, this_size_, and total_size_.

virtual Size protocols::frag_picker::quota::SecondaryStructurePool::size_left ( ) const

inlinevirtual

Says how many fragments can still be inserted into this pool.

Implements protocols::frag_picker::quota::QuotaPool.

References current_size(), and total_size().

virtual Size protocols::frag_picker::quota::SecondaryStructurePool::total_size ( ) const

inlinevirtual

Says how many fragments (in total) may fit into this pool.

Implements protocols::frag_picker::quota::QuotaPool.

References storage_.

Referenced by SecondaryStructurePool(), and size_left().

Member Data Documentation

Size protocols::frag_picker::quota::SecondaryStructurePool::buffer_factor_

private

Referenced by resize(), SecondaryStructurePool(), and set_fraction().

utility::vector1<Size> protocols::frag_picker::quota::SecondaryStructurePool::components_

private

Referenced by quota_score(), and SecondaryStructurePool().

char protocols::frag_picker::quota::SecondaryStructurePool::ss_type_

private

Referenced by add(), could_be_accepted(), get_ss_type(), print_report(), and SecondaryStructurePool().

BoundedQuotaContainerOP protocols::frag_picker::quota::SecondaryStructurePool::storage_

private

Referenced by add(), clear(), current_size(), get_candidates(), insert(), push(), resize(), SecondaryStructurePool(), set_fraction(), and total_size().

Size protocols::frag_picker::quota::SecondaryStructurePool::this_size_

private

Referenced by SecondaryStructurePool(), and set_fraction().

Size protocols::frag_picker::quota::SecondaryStructurePool::total_size_

private

Referenced by SecondaryStructurePool(), and set_fraction().

utility::vector1<Real> protocols::frag_picker::quota::SecondaryStructurePool::weights_

private

Referenced by quota_score(), and SecondaryStructurePool().

The documentation for this class was generated from the following files:

src/protocols/frag_picker/quota/SecondaryStructurePool.hh
src/protocols/frag_picker/quota/SecondaryStructurePool.cc

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation